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# PDB coordinate and psi, phi, omega angles

Dr. Mrigank mrigank at imtech.ernet.in
Tue Sep 28 09:45:59 EST 1993

```In article <9309211522.AA04663 at conch.senod.uwf.edu>, hhuang at CONCH.SENOD.UWF.EDU (Hong Huang) writes:
> Dear Netters:
>
> Could anybody be so kind to show my how to display the 3D protein structures
> which are in PDB's orthogonal coordinate system.  My problems are:
>
>    (1) How to map 3D coordinates to our 2D screen, is it done by Ray Tracing?
>    (2) What are psi, phi and omega angles?
>
> I know there are many excellent packages out there but the point are, I have to
> do it myself and I do not have biology background.
>
Hi

Ans: (1) It is done by taking the xy projection of the system. For depth
effect depth cueing , Elimination of hidden line - Z buffering
etc. are done. Read any std. Text book on computer graphics it
will have the details. If you can't find one in lib. I can send
the details[ only brief].

Ans: (2) Phi psi and omega are 3 torsion angles in peptide bond, which can
define entire 3-D structure of backbone. See below:

+-------------------+
|                   |
R  |  H            O   |  H
|  |  |            ||  |  |
N----Ca----C=-|=-N-----Ca-----C-=-|=-N--
||     ^ |     ^  |   ^     ^|
O      | |     |  R   |     ||
| |     |      |     ||
Peptide    |      |     ||
Bond|    Phi   Psi   Omega
|                   |
+-------------------+
Here Phi and Psi are flexible and can rotate freely (In reality no
so freely) and omega has partial double bond so is fixed around
180 degrees. Refer to any text on protein structure to get the
details. Or again if you want I can post the details to you.

--
Dr. Mrigank                       \/Phone  +91 172 45004 x216
Institute of Microbial Technology /\Email:  mrigank at imtech.ernet.in
P O Box 1304, Sector 39A          \/UUCP:...!uunet!sangam!vikram!imtech!mrigank
Chandigarh 160 014 India.         /\
==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+
-- When I feed the poor, they call me saint. When I ask why the poors do
not have food, they call me communist - Archbishop Camaran

```